{ "127729-21859591": { "datetime_modified":"20241101T133217", "datetime_start":"20241101T120000", "datetime_end":"20241101T130000", "has_end_time":1, "date_start":"2024-11-01", "date_end":"2024-11-01", "time_start":"12:00:00", "time_end":"13:00:00", "time_zone":"America\/Detroit", "event_title":"FSML Lecture Series: Discovery of cellular reprogramming methodology through single-cell foundation models", "occurrence_title":"", "combined_title":"FSML Lecture Series: Discovery of cellular reprogramming methodology through single-cell foundation models: Nicholas Galioto (University of Michigan)", "event_subtitle":"Nicholas Galioto (University of Michigan)", "event_type":"Lecture \/ Discussion", "event_type_id":"13", "description":"Venue: 2052 Walter E. Lay Auto Lab and\r\n\r\nZoom: https:\/\/umich.zoom.us\/j\/97823527756?pwd=H01BbvtuG5q02Wzb8LJvhUnvijlAIe.1\r\n\r\nAbstract: Cell reprogramming, the transformation of a cell from one cell type to another through the introduction of exogenous transcription factors (TFs), is a rapidly developing research area that could lead to groundbreaking therapeutic technologies in areas such as tissue regeneration, disease modeling, and personalized medicine. However, there still exist many challenges obstructing its practical viability. Discovering which TFs induce reprogramming requires a combinatorial search, and testing a single\r\ncandidate set of TFs experimentally can cost tens of thousands of dollars and take multiple months. Moreover, even when an effective set of TFs is known, cell conversion efficiency lies only around 5%.\r\n\r\nFaced with these challenges, researchers have developed computational surrogate models to rapidly explore the TF search space at a fraction of the cost of wet lab experimentation. Unfortunately, these models have seen limited success in practice due to the difficulty of capturing the complex gene-gene\r\ninteractions within the cell, most of which are still not well-understood. With the recent high-profile rise of transformer-based foundation models for natural language, researchers are now turning to the transformer to push past current performance limitations in a wide range of digital biology tasks, including cell reprogramming. Of particular interest in these models is the attention mechanism, which is potentially well-suited for capturing long-range gene-gene interactions at a higher fidelity than previously possible. In this talk, I will describe how the transformer architecture has been adapted for cellular biology and analyze the utility of one such model, Geneformer, in identifying TFs for cell reprogramming. Specifically, I will present the results of an in silico perturbation experiment for reprogramming fibroblast cells to hematopoietic stem cells and compare the outcomes to experimental results found in the literature. I will conclude the talk with a discussion of the drawbacks and limitations of the Geneformer model and provide an assessment of what will be needed in the future for digital biology to fully reap the benefits of large-scale foundation models.\r\n\r\nBio:\r\nNick Galioto is a second-year postdoctoral research fellow in the Department of Computational Medicine and Bioinformatics at the University of Michigan (UM). He received his PhD at UM in aerospace engineering in 2023 under the advising of Alex Gorodetsky and remained in the lab for an additional year as a postdoc. In the Gorodetsky lab, Nick researched how to use stochastic models of dynamical systems to improve system identification. Now, Nick works in the Rajapakse lab researching how to create data-driven models of the dynamics of cell reprogramming.", "occurrence_notes":null, "guid":"127729-21859591@events.umich.edu", "permalink":"http:\/\/events.umich.edu\/event\/127729", "building_id":"1000400", "building_name":"Walter E Lay Auto Lab", "campus_maps_id":"86", "room":"2052A", "location_name":"Walter E Lay Auto Lab", "has_livestream":0, "cost":"", "tags":["Generative Ai","Michigan Engineering","Phd Seminar","Rackham","Research","Science","big data","Biology","Computational Science","Engineering","Micde","Graduate School","Graduate Students"], "website":"https:\/\/umich.zoom.us\/j\/97823527756?pwd=H01BbvtuG5q02Wzb8LJvhUnvijlAIe.1", "sponsors":[ { "group_name":"Frontiers in Scientific Machine Learning (FSML)", "group_id":"5234", "website":"" }, { "group_name":"Michigan Institute for Computational Discovery and Engineering", "group_id":"3286", "website":"http:\/\/micde.umich.edu" } ], "image_url":"https:\/\/events.umich.edu\/media\/attachments\/2024\/10\/event_127729_original-1.png", "styled_images":{ "event_thumb":"https:\/\/events.umich.edu\/media\/cache\/event_thumb\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_large":"https:\/\/events.umich.edu\/media\/cache\/event_large\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_large_2x":"https:\/\/events.umich.edu\/media\/cache\/event_large_2x\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_large_lightbox":"https:\/\/events.umich.edu\/media\/cache\/event_large_lightbox\/media\/attachments\/2024\/10\/event_127729_original-1.png", "group_thumb":"https:\/\/events.umich.edu\/media\/cache\/group_thumb\/media\/attachments\/2024\/10\/event_127729_original-1.png", "group_thumb_square":"https:\/\/events.umich.edu\/media\/cache\/group_thumb_square\/media\/attachments\/2024\/10\/event_127729_original-1.png", "group_large":"https:\/\/events.umich.edu\/media\/cache\/group_large\/media\/attachments\/2024\/10\/event_127729_original-1.png", "group_large_lightbox":"https:\/\/events.umich.edu\/media\/cache\/group_large_lightbox\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_large_crop":"https:\/\/events.umich.edu\/media\/cache\/event_large_crop\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_list":"https:\/\/events.umich.edu\/media\/cache\/event_list\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_list_2x":"https:\/\/events.umich.edu\/media\/cache\/event_list_2x\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_grid":"https:\/\/events.umich.edu\/media\/cache\/event_grid\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_grid_2x":"https:\/\/events.umich.edu\/media\/cache\/event_grid_2x\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_feature_large":"https:\/\/events.umich.edu\/media\/cache\/event_feature_large\/media\/attachments\/2024\/10\/event_127729_original-1.png", "event_feature_thumb":"https:\/\/events.umich.edu\/media\/cache\/event_feature_thumb\/media\/attachments\/2024\/10\/event_127729_original-1.png" }, "occurrence_count":1, "first_occurrence":21859591 } , "88544-21836956": { "datetime_modified":"20260112T144046", "datetime_start":"20241101T120000", "datetime_end":"20241101T123000", "has_end_time":1, "date_start":"2024-11-01", "date_end":"2024-11-01", "time_start":"12:00:00", "time_end":"12:30:00", "time_zone":"America\/Detroit", "event_title":"Heartfulness Guided Meditation", "occurrence_title":"", "combined_title":"Heartfulness Guided Meditation: Pushyami Gundala", "event_subtitle":"Pushyami Gundala", "event_type":"Well-being", "event_type_id":"12", "description":"Heartfulness Guided Meditation is a weekly, drop-in program designed to help you Mental well-being. \r\n\r\nAll U-M students, faculty, and staff are welcome to participate in guided meditation practice with a trainer every Friday at noon over Zoom (details to join are provided below). No prior experience with meditation is required. \r\n\r\n*What will you learn?*\r\n\r\nThe guided meditation practice involves three simple steps: relaxation, rejuvenation, and meditation.\r\n\r\nRelaxation brings your body to a calm, steady posture creating a stillness at the physical level, and prepares the mind for meditation. We follow this with a rejuvenation method to detox the mind to let go of stress and complex emotions, and will leave you feeling light and refreshed. Lastly, learning to meditate by being mindful of your heart will connect you with yourself by listening to your heart\u2019s voice. \r\n\r\n*Why Meditate?*\r\n\r\nWhile physical fitness keeps our bodies in shape, meditation is an exercise for the mind and mental wellness. In addition to the measurable benefits mentally and physically, many people benefit from an unquantifiable inner poise and harmony. \r\n\r\n*Please take Learn to Meditate session if you are new to the practice. These sessions are offered Monthly.* https:\/\/events.umich.edu\/event\/128708\r\n\r\n*Event Details*\r\n\r\nHeartfulness Guided Meditation \r\nFridays from 12-12:30 p.m. ET (except during university season days \/ holidays)\r\nJoin Via Zoom Meeting\r\nRegister to receive Passcode (see \u201cRelated links\u201d\r\n\r\n\r\nThis wellness program is coordinated by ITS Teaching & Learning and provided at no cost by heartfulness.org.", "occurrence_notes":null, "guid":"88544-21836956@events.umich.edu", "permalink":"http:\/\/events.umich.edu\/event\/88544", "building_id":"", "building_name":"", "campus_maps_id":"", "room":"", "location_name":null, "has_livestream":0, "cost":"", "tags":["Free","Health & Wellness","Well-being"], "website":"https:\/\/events.umich.edu\/event\/128708", "sponsors":[ { "group_name":"Information and Technology Services (ITS)", "group_id":"1179", "website":"https:\/\/x.com\/umichTECH" } ], 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